When filling a gap with a new face edges do not seem to subdivide correctly
The most likely explanation is that the new faces normals are flipped.

In the image below, i created a cube, added a subdivision surface, and then flipped the normals on the top face. As you can see, the top face becomes sharp, but it is hard to see why. However, if you select it and do the "flip normals" command, it returns to normal.



This may not be your issue, but try selecting the affected faces and using either Flip Normals or Make Normals Consistent, and it will most likely fix your issue.